diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/improved-rdock/rdock_python3.patch')
| -rw-r--r-- | var/spack/repos/builtin/packages/improved-rdock/rdock_python3.patch | 276 |
1 files changed, 276 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/improved-rdock/rdock_python3.patch b/var/spack/repos/builtin/packages/improved-rdock/rdock_python3.patch new file mode 100644 index 0000000000..bedcadc5b4 --- /dev/null +++ b/var/spack/repos/builtin/packages/improved-rdock/rdock_python3.patch @@ -0,0 +1,276 @@ +diff -u -r -N a/bin/sdrmsd b/bin/sdrmsd +--- a/bin/sdrmsd 2020-10-15 13:34:27.000000000 +0900 ++++ b/bin/sdrmsd 2020-10-19 09:21:43.000000000 +0900 +@@ -11,7 +11,7 @@ + # Date: 08-11-2013 + + import math +-import pybel ++from openbabel import pybel + import numpy as npy + import optparse + +@@ -103,24 +103,24 @@ + return mappingpose[0] + + def parseArguments(): +- optparse.OptionParser.format_epilog = lambda self, formatter: self.epilog +- epilog = """Args: +- reference.sdf SDF file with the reference molecule. +- input.sdf SDF file with the molecules to be compared to reference.\n""" +- parser = optparse.OptionParser("usage: %prog [options] reference.sdf input.sdf", epilog=epilog) +- parser.add_option("-f", "--fit",dest="fit", action="store_true", default=False, ++ optparse.OptionParser.format_epilog = lambda self, formatter: self.epilog ++ epilog = """Args: ++ reference.sdf SDF file with the reference molecule. ++ input.sdf SDF file with the molecules to be compared to reference.\n""" ++ parser = optparse.OptionParser("usage: %prog [options] reference.sdf input.sdf", epilog=epilog) ++ parser.add_option("-f", "--fit",dest="fit", action="store_true", default=False, + help="Superpose molecules before RMSD calculation") +- parser.add_option("--threshold","-t",dest="threshold", action="store", nargs=1, ++ parser.add_option("--threshold","-t",dest="threshold", action="store", nargs=1, + help="Discard poses with RMSD < THRESHOLD with respect previous poses which where not rejected based on same principle. A Population SDField will be added to output SD with the population number.", type=float) +- parser.add_option("-o","--out", dest="outfilename", metavar="FILE", default=False, ++ parser.add_option("-o","--out", dest="outfilename", metavar="FILE", default=False, + help="If declared, write an output SDF file with the input molecules with a new sdfield <RMSD>. If molecule was fitted, the fitted molecule coordinates will be saved.") +- (options, args) = parser.parse_args() +- +- #Check we have two arguments +- if len(args) < 2: +- parser.error("Incorrect number of arguments. Use -h or --help options to print help.") ++ (options, args) = parser.parse_args() ++ ++ #Check we have two arguments ++ if len(args) < 2: ++ parser.error("Incorrect number of arguments. Use -h or --help options to print help.") + +- return options, args ++ return options, args + + def updateCoords(obmol, newcoords): + "Update OBMol coordinates. newcoords is a numpy array" +@@ -133,8 +133,8 @@ + for correct RMSD comparison. Only the lowest RMSD will be returned. + + Returns: +- If fit=False: bestRMSD (float) RMSD of the best matching mapping. +- If fit=True: (bestRMSD, molecCoordinates) (float, npy.array) RMSD of best match and its molecule fitted coordinates. ++ If fit=False: bestRMSD (float) RMSD of the best matching mapping. ++ If fit=True: (bestRMSD, molecCoordinates) (float, npy.array) RMSD of best match and its molecule fitted coordinates. + """ + mappings = pybel.ob.vvpairUIntUInt() + bitvec = pybel.ob.OBBitVec() +@@ -148,18 +148,18 @@ + posecoords = npy.array([atom.coords for atom in molec])[mappose] + resultrmsd = 999999999999 + for mapping in mappings: +- automorph_coords = [None] * len(targetcoords) +- for x, y in mapping: +- automorph_coords[lookup.index(x)] = targetcoords[lookup.index(y)] +- mapping_rmsd = rmsd(posecoords, automorph_coords) +- if mapping_rmsd < resultrmsd: +- resultrmsd = mapping_rmsd +- fitted_result = False +- if fit: +- fitted_pose, fitted_rmsd = superpose3D(npy.array(automorph_coords), npy.array(posecoords)) +- if fitted_rmsd < resultrmsd: +- resultrmsd = fitted_rmsd +- fitted_result = fitted_pose ++ automorph_coords = [None] * len(targetcoords) ++ for x, y in mapping: ++ automorph_coords[lookup.index(x)] = targetcoords[lookup.index(y)] ++ mapping_rmsd = rmsd(posecoords, automorph_coords) ++ if mapping_rmsd < resultrmsd: ++ resultrmsd = mapping_rmsd ++ fitted_result = False ++ if fit: ++ fitted_pose, fitted_rmsd = superpose3D(npy.array(automorph_coords), npy.array(posecoords)) ++ if fitted_rmsd < resultrmsd: ++ resultrmsd = fitted_rmsd ++ fitted_result = fitted_pose + + if fit: + return (resultrmsd, fitted_pose) +@@ -167,16 +167,16 @@ + return resultrmsd + + def saveMolecWithRMSD(outsdf, molec, rmsd, population=False): +- newData = pybel.ob.OBPairData() ++ newData = pybel.ob.OBPairData() + newData.SetAttribute("RMSD") + newData.SetValue('%.3f'%rmsd) + + if population: +- popData = pybel.ob.OBPairData() +- popData.SetAttribute("Population") +- popData.SetValue('%i'%population) +- molec.OBMol.CloneData(popData) +- ++ popData = pybel.ob.OBPairData() ++ popData.SetAttribute("Population") ++ popData.SetValue('%i'%population) ++ molec.OBMol.CloneData(popData) ++ + molec.OBMol.CloneData(newData) # Add new data + outsdf.write(molec) + +@@ -184,13 +184,13 @@ + import sys, os + + (opts, args) = parseArguments() +- ++ + xtal = args[0] + poses = args[1] + + if not os.path.exists(xtal) or not os.path.exists(poses): +- sys.exit("Input files not found. Please check the path given is correct.") +- ++ sys.exit("Input files not found. Please check the path given is correct.") ++ + fit = opts.fit + outfname = opts.outfilename + threshold = opts.threshold +@@ -202,71 +202,71 @@ + + #If outfname is defined, prepare an output SDF sink to write molecules + if outfname: +- outsdf = pybel.Outputfile('sdf', outfname, overwrite=True) ++ outsdf = pybel.Outputfile('sdf', outfname, overwrite=True) + + # Find the RMSD between the crystal pose and each docked pose + dockedposes = pybel.readfile("sdf", poses) +- if fit: print "POSE\tRMSD_FIT" +- else: print "POSE\tRMSD_NOFIT" ++ if fit: print ("POSE\tRMSD_FIT") ++ else: print ("POSE\tRMSD_NOFIT") + skipped = [] +- moleclist = {} # Save all poses with their dockid +- population = {} # Poses to be written ++ moleclist = {} # Save all poses with their dockid ++ population = {} # Poses to be written + outlist = {} + for docki, dockedpose in enumerate(dockedposes): + dockedpose.removeh() +- natoms = len(dockedpose.atoms) +- if natoms != crystalnumatoms: +- skipped.append(docki+1) +- continue +- if fit: +- resultrmsd, fitted_result = getAutomorphRMSD(crystal, dockedpose, fit=True) +- updateCoords(dockedpose, fitted_result) +- else: +- resultrmsd = getAutomorphRMSD(crystal, dockedpose, fit=False) +- +- if threshold: +- # Calculate RMSD between all previous poses +- # Discard if rmsd < FILTER threshold +- if moleclist: +- match = None +- bestmatchrmsd = 999999 +- for did,prevmol in moleclist.iteritems(): +- tmprmsd = getAutomorphRMSD(prevmol, dockedpose) +- if tmprmsd < threshold: +- if tmprmsd < bestmatchrmsd: +- bestmatchrmsd = tmprmsd +- match = did +- +- if match != None: +- # Do not write this one +- # sum one up to the matching previous molecule id +- print >> sys.stderr, "Pose %i matches pose %i with %.3f RMSD"%(docki+1, match+1, bestmatchrmsd) +- population[match] += 1 +- else: +- # There's no match. Print info for this one and write to outsdf if needed +- # Save this one! +- if outfname: outlist[docki] = (dockedpose, resultrmsd) +- print "%d\t%.2f"%((docki+1),resultrmsd) +- moleclist[docki] = dockedpose +- population[docki] = 1 +- else: +- # First molecule in list. Append for sure +- moleclist[docki] = dockedpose +- population[docki] = 1 +- if outfname: outlist[docki] = (dockedpose, resultrmsd) +- else: +- # Just write best rmsd found and the molecule to outsdf if demanded +- if outfname: saveMolecWithRMSD(outsdf, dockedpose, resultrmsd) +- print "%d\t%.2f"%((docki+1),resultrmsd) ++ natoms = len(dockedpose.atoms) ++ if natoms != crystalnumatoms: ++ skipped.append(docki+1) ++ continue ++ if fit: ++ resultrmsd, fitted_result = getAutomorphRMSD(crystal, dockedpose, fit=True) ++ updateCoords(dockedpose, fitted_result) ++ else: ++ resultrmsd = getAutomorphRMSD(crystal, dockedpose, fit=False) ++ ++ if threshold: ++ # Calculate RMSD between all previous poses ++ # Discard if rmsd < FILTER threshold ++ if moleclist: ++ match = None ++ bestmatchrmsd = 999999 ++ for did,prevmol in moleclist.iteritems(): ++ tmprmsd = getAutomorphRMSD(prevmol, dockedpose) ++ if tmprmsd < threshold: ++ if tmprmsd < bestmatchrmsd: ++ bestmatchrmsd = tmprmsd ++ match = did ++ ++ if match != None: ++ # Do not write this one ++ # sum one up to the matching previous molecule id ++ print >> sys.stderr, "Pose %i matches pose %i with %.3f RMSD"%(docki+1, match+1, bestmatchrmsd) ++ population[match] += 1 ++ else: ++ # There's no match. Print info for this one and write to outsdf if needed ++ # Save this one! ++ if outfname: outlist[docki] = (dockedpose, resultrmsd) ++ print ("%d\t%.2f"%((docki+1),resultrmsd)) ++ moleclist[docki] = dockedpose ++ population[docki] = 1 ++ else: ++ # First molecule in list. Append for sure ++ moleclist[docki] = dockedpose ++ population[docki] = 1 ++ if outfname: outlist[docki] = (dockedpose, resultrmsd) ++ else: ++ # Just write best rmsd found and the molecule to outsdf if demanded ++ if outfname: saveMolecWithRMSD(outsdf, dockedpose, resultrmsd) ++ print ("%d\t%.2f"%((docki+1),resultrmsd)) + + if outlist: +- # Threshold applied and outlist need to be written +- for docki in sorted(outlist.iterkeys()): +- molrmsd = outlist[docki] +- # Get number of matchs in thresholding operation +- pop = population.get(docki) +- if not pop: pop = 1 +- # Save molecule +- saveMolecWithRMSD(outsdf, molrmsd[0], molrmsd[1], pop) +- +- if skipped: print >> sys.stderr, "SKIPPED input molecules due to number of atom missmatch: %s"%skipped ++ # Threshold applied and outlist need to be written ++ for docki in sorted(outlist.iterkeys()): ++ molrmsd = outlist[docki] ++ # Get number of matchs in thresholding operation ++ pop = population.get(docki) ++ if not pop: pop = 1 ++ # Save molecule ++ saveMolecWithRMSD(outsdf, molrmsd[0], molrmsd[1], pop) ++ ++ if skipped: print("SKIPPED input molecules due to number of atom missmatch: %s"%skipped, file=sys.stderr) +diff -u -r -N a/build/test/RBT_HOME/check_test.py b/build/test/RBT_HOME/check_test.py +--- a/build/test/RBT_HOME/check_test.py 2020-10-14 11:48:36.000000000 +0900 ++++ b/build/test/RBT_HOME/check_test.py 2020-10-19 09:23:31.000000000 +0900 +@@ -21,6 +21,6 @@ + error = 1 + + if error == 1: +- print "The test failed, please check the compilation is OK and no errors were raised." ++ print ("The test failed, please check the compilation is OK and no errors were raised.") + else: +- print "The test succeeded! The results agree with the reference ones.\nHave fun using rDock!!" ++ print ("The test succeeded! The results agree with the reference ones.\nHave fun using rDock!!") |